In 2012, Ellison began rapping under the persona Captain Murphy, based on the Sealab 2021 character of the same name. Ellison kept this fact a secret for several months, finally revealing his identity several weeks after the release of his first rap mixtape, Duality.[8]

Around this time, he was interning at the pioneering hip hop label Stones Throw Records. Days were spent in their offices, and nights were spent at his grandmothers, working on the music that would become his debut album: 1983. The record (released on LA indie label Plug Research) was an early touchstone for Ellison's eclectic creative mission, forging compressed, spacey and Eastern sounding hip-hop beats, that summoned Madlib as much as Dntel, while sampling as far back as 70sJapanese proto-synthpop and 60sjazz harp. It would also feature Laura Darlington, who went on to become a vocal fixture of future albums.[citation needed]

His first release on Warp, Reset EP, gave his new audience a taste of the steady grooves and darker breaks that had earned him the move. As Ellison's profile rose, he decided to commandeer the limelight by launching his own label, Brainfeeder, to house his friends (Samiyam, Ras G, etc.) and unite a large section of the LA beat scene under one label.

2008–09: Los Angeles and Brainfeeder

In 2008 Flying Lotus released Los Angeles, a 17-track album dedicated to his home city. The album captured the abundant styles of his city in seventeen bullet sized tracks, that harked back to golden era hip hop while innovating in its endeavours to introduce recalibrated shards of bass, techno and soul, plus samples of his own Aunt's harp playing. Telling Quietus on the subject of J Dillas influence on his music: "I love Dilla and who knows where this beat thing would be without him. His work ethic inspired so many producers around the world, but when he moved out to LA, it seemed that his presence here inspired everyone to kick things into overdrive. If I had to describe his music, I'd say it were 'imaginative soul music'. I think it's his imagination that appeals to me, personally. Dilla could flip a boring record and make you feel like you were flying."

2008 saw Ellison enter a stage of hyper-productivity, as he followed up the Los Angeles record with collaborative tracks with Samiyam and Gonjasufi, a limited white label run of remixes ("Camel", "Lightworks", R2-D2 sound effects, "Shadows of Tomorrow" and "Promiscuous") called Shhh!, and a series of LA inspired EPs. Each of the La EPs features remixes and unreleased tracks from his Los Angeles Album. The third in that series (titled L.A. EP 3 X 3), marked a new atmospheric style in his sound.

The same year, Flying Lotus also remixed "Reckoner" from Radiohead's album In Rainbows.[16]

2010–11: Cosmogramma and collaborations

His third studio album, Cosmogramma, was released in the UK on May 3, 2010, and in the US on May 4, 2010.[17] In January 2011, Cosmogramma won in the Dance/Electronica Album category in the 10th Annual Independent Music Awards.[18] The multi-award-winning Cosmogramma was a hard-hitting afrofuturistic shrine to soul, hip-hop, jazz and IDM but, with more emphasis on a lyrical message than ever before, it was also a cathartic grieving experience. The album was accompanied by live instrumentation (Thundercat on bass, Miguel Atwood Ferguson on strings, Rebekah Raff on harp) and live vocalists (Thom Yorke, Laura Darlington) - all picked to help communicate the spiritual musical lineage of Ellison’s family (Ravi Coltrane, himself, played tenor sax). Stephen Bruner, aka Thundercat, who is featured extensively on Cosmogramma, would later become a large part of future albums by Flying Lotus.

In 2010, Flying Lotus collaborated with the Ann Arbor Film Festival in the performance of a live scoring of the 1962 avant-garde film Heaven and Earth Magic.[19] In a post-viewing interview with the audience, Flying Lotus said that he was unsure whether or not a recording of the performance (or a recreation of it) would be publicly released, but he would be enthusiastic toward similar projects in the future. He was chosen by Battles to perform at the ATP Nightmare Before Christmas festival that it co-curated in December 2011 in Minehead, England, UK.[20]

In September 2010, Flying Lotus released "Pattern+Grid World", an 8 track EP featuring Thundercat on bass & art by Theo Ellsworth. The Track Camera Day was used in the Killer Mike song Swimming, which was released as part of the Adult Swim Singles Series.

In January 2011, Flying Lotus won the 10th Annual Independent Music Awards for his video "MmmHmm" in the Short-Form Video category.[21]

It was reported in 2011 that Flying Lotus would be collaborating with R&B singer Erykah Badu on new material for her next album,[22] and planned to remix one of Radiohead's songs from The King of Limbs.[23]

2012–13: Until the Quiet Comes and Captain Murphy

With a lifelong fascination for hip hop, but no firm position within it, the likes of Odd Future (also aficionados of Adult Swim), A$AP Mob, Spaceghostpurrp and Shabazz Palaces inspired him to get a bit more direct, and soon he was knocking out production for Odd Future’s Hodgy Beats’ Untitled EP. While with Hodgy, he had a moment of rap enlightenment: "I can recall the moment specifically. I haven’t told anybody this and I am so glad to talk to you about it. I feel like it was such a big deal for me personally. [Odd Future] started playing me some of The OF Tape Vol. 2. I asked them, 'Yo, Hodgy, how long did it take you to record this shit? How long did it take you to write this song?' 'Aw, my nigga, it took me like 15 minutes.’ 15 minutes? Are you fucking serious? I was like, 'Nah, nigga. I am gonna do this shit.'" Throughout the summer of 2012, Captain Murphy would make golden-caped appearances, dressed in Luchadore Ensemble, with his true identity masked to the public.

In August 2012, Flying Lotus announced a multimedia project with filmmaker Miwa Matreyek, which is to be titled The Mapping of Countries Yet to Come.[24]

Behind closed doors though, the work for his fourth album Until the Quiet Comes was pretty much done. A year prior, Ellison had worked with Ann Arbor Festival to live score a surreal and avant-garde 50s animation Heaven and Earth Magic (pictured below), and a fascination with dreamlike states had continued into this record. Until The Quiet Comes continued his creative relationship with Radiohead's Thom Yorke, as well as Jonny Greenwood, Niki Randa, Erykah Badu, Laura Darlington and, of course, Thundercat, and was cinematically captured in a short film by Kahlil Joseph.

In late 2012, less than two months after the release of his last record, a website started circulating online: www.captainmurphy.xxx. Press speculated who the rapper was, with guessing being centered around the Odd Future Crew. The site hosted Duality, a 34-minute short film mixtape, that comprised both new material and tracks that had been leaking all summer.

In April 2013, Flying Lotus announced that he has his own radio station in the video gameGrand Theft Auto V, saying there would be "a ton of new songs and information, including rapping a new Captain Murphy song produced by Hudson Mohawke".[27]

On July 17, 2013, Flying Lotus announced on Twitter that he had been nominated for a VMA for the song "Tiny Tortures".[28]

2014–2015: You're Dead!

On July 15, 2014, Flying Lotus posted on Instagram a photo of vinyl test pressings labeled "LP #5".[29] On July 22, he announced that his fifth studio album, You're Dead!, would be released in the UK on October 6, 2014, and in the US on October 7, 2014.[30] The album features guest appearances by Kendrick Lamar, Snoop Dogg and Herbie Hancock.

On August 15, 2014, Flying Lotus released a new song called "Cosplay" with his alias Captain Murphy.[31]

On September 30, 2014, Flying Lotus scored the short film A Portrait of Noomi Rapace, starring actress Noomi Rapace and directed by Aitor Throup.[32]

2016–present: Kuso

On July 5, 2016, Ellison announced the start of Brainfeeder film division.[36] Shortly after, at the Sundance NEXT festival, he premiered a short film titled Royal. It was later revealed to be part of his feature film directorial debut, Kuso.[37]Kuso would star Hannibal Buress, Tim Heidecker and David Firth among others.[38]Kuso featured new music from Ellison himself under both the Flying Lotus and Captain Murphy names, Aphex Twin, Busdriver, and Thundercat, among others.[39][40]Kuso premiered at the Sundance Film Festival in 2017. On June 6, 2017, Ellison announced that Kuso would be released via the horror video streaming service Shudder, on July 21, 2017.[41]Kuso was also confirmed a theatrical release in New York City and Los Angeles. Addressing the responsibility of the wide release of Kuso, on Twitter, Ellison praised Shudder, explaining he found it to be a suitable home for the film's release.[42]

On November 2, 2017, Ellison released a music video for a new song of his, "Post Requisite", and is "currently finishing his next studio album on Warp”.[43] He also wrote the soundtrack for the 2017 short film Blade Runner 2022.